An improved quantum biochemistry description of the glutamate–GluA2 receptor binding within an inhomogeneous dielectric function framework

2017 ◽  
Vol 41 (14) ◽  
pp. 6167-6179 ◽  
Author(s):  
A. C. V. Martins ◽  
P. de-Lima-Neto ◽  
E. W. S. Caetano ◽  
V. N. Freire
Keyword(s):  
Dielectric Constant ◽  
Dielectric Function ◽  
Receptor Binding ◽  
Electrostatic Interaction ◽  
Protein Residues ◽  
Inhomogeneous Dielectric

A new methodology to define the inhomogeneous dielectric constant of protein residues, to apply to the calculation of protein–ligand properties such as the electrostatic interaction.

scholarly journals On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function

2014 ◽  
Vol 13 (03) ◽  
pp. 1440002 ◽  
Author(s):  
Lin Li ◽  
Chuan Li ◽  
Emil Alexov
Keyword(s):  
Dielectric Constant ◽  
Dielectric Function ◽  
Solvation Energy ◽  
Bulk Water ◽  
Dielectric Medium ◽  
Water Phase ◽  
Polar Component ◽  
Implicit Methods ◽  
Inhomogeneous Dielectric ◽  
Polar Solvation

Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule–water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (Li L, Li C, Zhang Z, Alexor E, On the dielectric constant of proteins: Smooth dielectric function for macromolecular modeling and its implementation in Delphi, J Chem Theory Comput9(4):2126–2136, 2013). Here we examine various aspects of the modeling of polar solvation energy in such inhomogeneous systems in terms of the solute–water boundary and the inhomogeneity of the solute in the absence of water surrounding. The smooth Gaussian-based dielectric function is implemented in the DelPhi finite-difference program, and therefore the sensitivity of the results with respect to the grid parameters is investigated, and it is shown that the calculated polar solvation energy is almost grid independent. Furthermore, the results are compared with the standard two-media model and it is demonstrated that on average, the standard method overestimates the magnitude of the polar solvation energy by a factor 2.5. Lastly, the possibility of the solute to have local dielectric constant larger than of a bulk water is investigated in a benchmarking test against experimentally determined set of pKa's and it is speculated that side chain rearrangements could result in local dielectric constant larger than 80.

SCATTERING FROM A CYLINDER COATED WITH AN INHOMOGENEOUS DIELECTRIC SHEATH

1963 ◽  
Vol 41 (1) ◽  
pp. 143-151 ◽  
Author(s):  
C. Yeh ◽  
Z. A. Kaprielian
Keyword(s):  
Dielectric Constant ◽  
Scattering Problem ◽  
Plane Waves ◽  
Space Vehicle ◽  
Plasma Sheath ◽  
Scattering Coefficients ◽  
Average Value ◽  
Inhomogeneous Dielectric ◽  
Specific Variation ◽  
Plane Wave Scattering

As a space vehicle re-enters the atmosphere, a plasma sheath, surrounding the vehicle, is generated. It is well known that the sheath is inhomogeneous. However, to make this problem suitable for theoretical analysis, most investigators make the assumption that the sheath is homogeneous. To investigate the validity of this assumption, the idealized problem of the scattering of plane waves by a conducting cylinder coated with a stratified dielectric sheath is considered. The wave equation is separated using the vector wave-function method of Hansen and Stratton. It is then applied to the plane-wave scattering problem. The backscattering cross section is defined and obtained. Analytical expressions for the scattering coefficients of a thin inhomogeneous sheath are also given. Numerical computations are carried out for a specific variation of the dielectric sheath: i.e., ε(r) = ε0α/k0r, where α is a constant, k02 = ε2 με0, and ε0 is the free-space dielectric constant. Results are compared with the homogeneous sheath problem; the dielectric constant of the homogeneous sheath is taken to be the average value of that for the inhomogeneous sheath. It is found that in general rather distinct differences are observed except when the sheath is very thin.

Measurement of the dielectric function spectra of low dielectric constant using the spectroscopic ellipsometry

2003 ◽  
Author(s):  
Masahiro Horie ◽  
Kamil Postava ◽  
Tomuo Yamaguchi ◽  
Kumiko Akashika ◽  
Hideki Hayashi ◽  
...  
Keyword(s):  
Dielectric Constant ◽  
Dielectric Function ◽  
Spectroscopic Ellipsometry ◽  
Low Dielectric Constant ◽  
Low Dielectric

scholarly journals Modeling the Bulk and Nanometric Dielectric Functions of Au and Ag

2021 ◽  
Author(s):  
Brahim Ait Hammou ◽  
Abdelhamid El Kaaouachi ◽  
Abdellatif El Oujdi ◽  
Adil Echchelh ◽  
Said Dlimi ◽  
...  
Keyword(s):  
Dielectric Constant ◽  
Dielectric Function ◽  
Imaginary Part ◽  
Complex Number ◽  
Theoretical Models ◽  
Electronic Transitions ◽  
Experimental Measurements ◽  
Mathematical Functions ◽  
Lorentz Theory ◽  
Critical Model

In this work, we model the dielectric functions of gold (Au) and silver (Ag) which are typically used in photonics and plasmonics. The modeling has been performed on Au and Ag in bulk and in nanometric states. The dielectric function is presented as a complex number with a real part and an imaginary part. First, we will model the experimental measurements of the dielectric constant as a function of the pulsation ω by appropriate mathematical functions in an explicit way. In the second part we will highlight the contributions to the dielectric constant value due to intraband and interband electronic transitions. In the last part of this work we model the dielectric constant of these metals in the nanometric state using several complex theoretical models such as the Drude Lorentz theory, the Drude two-point critical model, and the Drude three-point critical model. We shall comment on which model fits the experimental dielectric function best over a range of pulsation.

Optical properties of pure and TM-doped single-walled ZnO nanotubes (8,0) (TM = V and Co) by first principles calculations

2016 ◽  
Vol 30 (01) ◽  
pp. 1550255 ◽  
Author(s):  
R. Taghavi Mendi ◽  
M. Majidiyan Sarmazdeh ◽  
A. Boochani ◽  
S. M. Elahi ◽  
S. Naderi
Keyword(s):  
Dielectric Constant ◽  
Optical Properties ◽  
Energy Range ◽  
Dielectric Function ◽  
Optical Conductivity ◽  
Optical Transitions ◽  
Optical Reflectivity ◽  
Zno Nanotubes ◽  
Low Energies ◽  
Co Doped

In this paper, some optical properties of pure and transition metal-doped (TM = Co and V) single-walled ZnO nanotubes (8,0) (SWZnONT(8,0)) such as, real and imaginary parts of the dielectric function, optical conductivity, refractive index and optical reflectivity, were investigated. The calculations have been performed within framework of the density functional theory (DFT) using the full potential linearized augmented plane wave (FP-LAPW) and the generalized gradient approximation (GGA). The results show that, optical properties of SWZnONT(8,0) are anisotropic, especially at low energies and this anisotropy at low energies increases with doping of V in SWZnONT(8,0) while the Co-doped SWZnONT(8,0) behaves like pure SWZnONT(8,0). Doping of ZnO nanotubes has a significant impact on the value of the dielectric constant, so that due to the presence of V atom, the dielectric constant is increased up to three times. Study of the imaginary part of the dielectric function and optical conductivity showed that the important energy range for absorption processes and optical transitions is low energy range to 15 eV. The optical transitions have been studied based on band structure and density of states. The results of the optical reflectivity showed that these nanotubes are transparent in a wide energy ranges which provide them for using in transparent coatings. In addition, due to the reported magnetic properties for V- and Co-doped ZnO nanotubes, these nanotubes are suitable for using in spintronics and magneto-optic devices.

Complex solutions under shear and pressure: a rheometer setup for X-ray scattering experiments

2017 ◽  
Vol 24 (3) ◽  
pp. 646-652 ◽  
Author(s):  
D. C. F. Wieland ◽  
T. Zander ◽  
V. M. Garamus ◽  
C. Krywka ◽  
A. Dedinaite ◽  
...  
Keyword(s):  
Dielectric Constant ◽  
High Pressure ◽  
Electrostatic Interaction ◽  
The Body ◽  
X Ray ◽  
X Ray Scattering ◽  
Joint Lubrication ◽  
Complex Solutions ◽  
Ray Scattering

A newly developed high-pressure rheometer forin situX-ray scattering experiments is described. A commercial rheometer was modified in such a way that X-ray scattering experiments can be performed under different pressures and shear. First experiments were carried out on hyaluronan, a ubiquitous biopolymer that is important for different functions in the body such as articular joint lubrication. The data hint at a decreased electrostatic interaction at higher pressure, presumably due to the increase of the dielectric constant of water by 3% and the decrease of the free volume at 300 bar.

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